Gene Ontology analysis of differentially expressed genes. Gingival fibroblasts were cultured with or without TNFα (20 ng/ml), and cDNA samples were hybridized to an oligonucleotide microarray. Enrichment analysis was performed to identify biological themes among the genes that were differentially expressed in the different comparisons. The plot shows a selection of the gene ontology (GO) categories that were overrepresented among the genes having a significant change in expression between 1 h and 3 h due to TNFα treatment. The color of each node illustrates significance and can be interpreted in the scale bar, which displays the false discovery rate on a log10 scale. Arrows indicate the parent to child direction. For clarity, due to space reasons the figure does not include all significant GO categories. Complete lists of significant GO categories for the different comparisons can be found in the additional material (Additional files 2, 5 and 8).